Spinal cord data

Morphometry

Code imports

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

Archive:  spinalcord_results.zip
  inflating: data/spine/DWI_RD.csv   
  inflating: data/spine/DWI_FA.csv   
  inflating: data/spine/csa-SC_T2w.csv  
  inflating: data/spine/DWI_MD.csv   
  inflating: data/spine/MTR.csv      
  inflating: data/spine/MTsat.csv    
  inflating: data/spine/csa-GM_T2s.csv  
  inflating: data/spine/csa-SC_T1w.csv  
  inflating: data/spine/._csa-SC_T1w.csv  
  inflating: data/spine/T1.csv       

--2022-06-15 01:54:04--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.114.3
Connecting to github.com (github.com)|140.82.114.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220615%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220615T015404Z&X-Amz-Expires=300&X-Amz-Signature=cd7aa08e732e93e40ba060857a9fff5b51950d56e622119b1f6ea63db3459ed9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-15 01:54:04--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220615%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220615T015404Z&X-Amz-Expires=300&X-Amz-Signature=cd7aa08e732e93e40ba060857a9fff5b51950d56e622119b1f6ea63db3459ed9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... ........                                   100% 7.92M=0.002s

2022-06-15 01:54:04 (7.92 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]

Load data plot it

dataset.load()

fig_spine = Plot(dataset, plot_name = 'spine-1')

fig_spine.title = 'Spinal cord morphometry'

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book')

Quantitative MRI

data_type = 'qmri'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

Archive:  spinalcord_results.zip
  inflating: data/qmri/DWI_RD.csv    
  inflating: data/qmri/DWI_FA.csv    
  inflating: data/qmri/csa-SC_T2w.csv  
  inflating: data/qmri/DWI_MD.csv    
  inflating: data/qmri/MTR.csv       
  inflating: data/qmri/MTsat.csv     
  inflating: data/qmri/csa-GM_T2s.csv  
  inflating: data/qmri/csa-SC_T1w.csv  
  inflating: data/qmri/._csa-SC_T1w.csv  
  inflating: data/qmri/T1.csv        

--2022-06-15 01:54:04--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.114.3
Connecting to github.com (github.com)|140.82.114.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220615%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220615T015404Z&X-Amz-Expires=300&X-Amz-Signature=cd7aa08e732e93e40ba060857a9fff5b51950d56e622119b1f6ea63db3459ed9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-15 01:54:04--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220615%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220615T015404Z&X-Amz-Expires=300&X-Amz-Signature=cd7aa08e732e93e40ba060857a9fff5b51950d56e622119b1f6ea63db3459ed9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... ........                                   100% 13.5M=0.001s

2022-06-15 01:54:04 (13.5 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]

dataset.load()

fig_spine = Plot(dataset, plot_name = 'spine-2')
fig_spine.title = 'Spinal cord qMRI measures'

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book')